Aug 30, 2024

Public workspacePreparing 10X Genomics CytAssist FFPE Sections

DOI
dx.doi.org/10.17504/protocols.io.n92ldme3ol5b/v1
  • 1Brain and Mind Centre & Faculty of Medicine and Health School of Medical Sciences, The University of Sydney, Sydney, NSW 2050, Australia;
  • 2Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
YuHong Fu
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DOI: dx.doi.org/10.17504/protocols.io.n92ldme3ol5b/v1
Protocol Citation: YuHong Fu, Glenda Halliday 2024. Preparing 10X Genomics CytAssist FFPE Sections. protocols.io https://dx.doi.org/10.17504/protocols.io.n92ldme3ol5b/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: January 11, 2024
Last Modified: August 30, 2024
Protocol Integer ID: 93359
Keywords: FFPE, 10X, Sectioning, ASAPCRN
Funders Acknowledgement:
The Michael J. Fox Foundation for Parkinson’s Research (MJFF) and the Aligning Science Across Parkinson’s (ASAP) initiative
Grant ID: ASAP-020529
The Michael J. Fox Foundation for Parkinson’s Research (MJFF) and the Aligning Science Across Parkinson’s (ASAP) initiative
Grant ID: ASAP-020505
Abstract
Designing and properly mounting FFPE sections on large-window CytAssist slides is important for downstream analysis and data quality. This protocol describes the key steps for this preparation.
Set-up before cutting FFPE sections
Set-up before cutting FFPE sections
Clean the surface of the bench area, microtome (HistoCore MULTICUT R, Leica), Water bath (HI1210, Leica), and tools (including forceps and blades) with 80% ethanol.
10m
Spray RNase ZapTM (Thermo Fisher Scientific) on the surface of the bench area, instruments, and tools and leave them to completely dry before use.
30m
Filled the Water bath with RNAse/DNAse free water and set the temperature at 40℃.
30m
Cut FFPE sections
Cut FFPE sections
1d 4h 15m
1d 4h 15m
Cut FFPE sections at 6um thickness.
Note: The time cost indicated for this step is for one FFPE block.
15m
Mount sections in the center region (< 11mm x 11mm) of the poly-prep slide according to the 10X genomics analysis requirement.
Note: The time cost for this step is experiment task-dependent.
4h
Incubated mounted sections at 42°C for 3 h and dried overnight at room temperature in a desiccator. 
1d
Ready for downstream CytAssist procedure.